Lookup Dataset

Overview

The lookup/ dataset contains controlled vocabularies and standardized crosswalks used across the Pristine Seas Science Database. These tables ensure consistency in traits, classification, and code mappings across survey methods and spatial units.

Each table is documented in the section where it is used. This page provides a centralized index of all lookup tables.

Table Index

Table	Description	Used In
`lookup.functional_groups`	Classifies benthic taxa into functional groups (e.g., coral, CCA, turf).	`uvs.lpi_cover_by_taxa`
`lookup.depth_strata`	Binning rules for assigning stations to standardized depth categories.	All `uvs.*_stations` tables
`lookup.habitat_types`	Standardized vocabulary for reef habitat types (e.g., fore reef, patch reef).	`uvs.sites`, `uvs.stations`
`lookup.exposure_types`	Controlled values for exposure conditions (e.g., windward, leeward, lagoon).	`uvs.sites`, `uvs.stations`
`lookup.benthic_codes`	Maps field morphotaxa to standardized taxonomic names and functional groups.	`uvs.lpi_counts`
`lookup.fisheries_use`	Fishery importance classifications from FishBase and expert sources.	`taxonomy.fish`

See each protocol section for details and schema examples.

--- title: "Lookup Dataset" format: html: theme: lux self-contained: true code-fold: true toc: true toc-depth: 3 toc-location: right number-sections: false --- ```{r setup, message = F, warning = F, fig.width = 10, fig.height = 10, echo = F} options(scipen = 999) library(PristineSeasR) library(bigrquery) library(gt) library(gtExtras) library(tibble) library(tidyverse) library(dplyr) library(ggplot2) library(plotly) library(lubridate) knitr::opts_chunk$set(eval = F, warning = F, message = F, include = F, echo = F) ps_paths <- PristineSeasR::get_sci_drive_paths() prj_path <- file.path(ps_paths$projects, "legacy-db") ps_data_path <- ps_paths$datasets bigrquery::bq_auth(email = "marine.data.science@ngs.org") project_id <- "pristine-seas" bq_connection <- DBI::dbConnect(bigrquery::bigquery(), project = project_id) ``` #### Overview The `lookup/` dataset contains controlled vocabularies and standardized crosswalks used across the Pristine Seas Science Database. These tables ensure consistency in traits, classification, and code mappings across survey methods and spatial units. Each table is documented in the section where it is used. This page provides a centralized index of all lookup tables. --- #### Table Index ```{r eval = T, include = T} library(gt) lookup_index <- tribble( ~Table, ~Description, ~Used_in, "`lookup.functional_groups`", "Classifies benthic taxa into functional groups (e.g., coral, CCA, turf).", "[`uvs.lpi_cover_by_taxa`](lpi.qmd)", "`lookup.depth_strata`", "Binning rules for assigning stations to standardized depth categories.", "All `uvs.*_stations` tables", "`lookup.habitat_types`", "Standardized vocabulary for reef habitat types (e.g., fore reef, patch reef).", "`uvs.sites`, `uvs.stations`", "`lookup.exposure_types`", "Controlled values for exposure conditions (e.g., windward, leeward, lagoon).", "`uvs.sites`, `uvs.stations`", "`lookup.benthic_codes`", "Maps field morphotaxa to standardized taxonomic names and functional groups.", "`uvs.lpi_counts`", "`lookup.fisheries_use`", "Fishery importance classifications from FishBase and expert sources.", "`taxonomy.fish`" ) gt(lookup_index) |> cols_label( Table = md("**Table**"), Description = md("**Description**"), Used_in = md("**Used In**") ) |> cols_width( Table ~ px(200), Description ~ px(400), Used_in ~ px(250) ) |> tab_options(table.font.size = px(13)) |> fmt_markdown(columns = everything()) |> gt_theme_nytimes() ``` > See each protocol section for details and schema examples.